Compositions and methods for detection of salmonella species

ABSTRACT

Described are compositions, methods and kits for detection and/or differential detection of serovars of  Salmonella enterica  subsp.  enterica  serovar such as S. Heidelberg and S. Hadar in samples. Some embodiments relate to multiplex amplification based molecular assays.

CROSS-REFERENCE(S) TO RELATED APPLICATION

This application is a divisional of U.S. application Ser. No. 13/788,715filed Mar. 7, 2013, which claims priority under 35 U.S.C. §119(e) ofU.S. Provisional Application No. 61/701,316 filed Sep. 14, 2012, theentire contents of which are incorporated herein by reference.

FIELD

The present disclosure, in some embodiments, relates to compositions,methods and kits for detection of a Salmonella enterica subsp. entericaserovar microorganism contaminant in a sample. Some embodiments describecompositions, methods and kits for differentially detecting a Salmonellaenterica subsp. enterica serovar Heidelberg (S. Heidelberg)microorganism. Some embodiments describe compositions, methods and kitsfor differentially detecting a Salmonella enterica subsp. entericaserovar Hadar (S. Hadar) microorganism.

BACKGROUND

Identification of bacterial contamination in food often occurssubsequent to an outbreak of a foodborne illness. Bacteria of Salmonellaenterica subsp. enterica serovars are frequently identified as a foodcontaminant of many foodborne illnesses.

Ingestion of S. Heidelberg and S. Hadar can result in Salmonellosis.Salmonellosis is characterized by diarrhea, fever, and abdominal crampsthat typically arise 12 to 72 hours after infection. Salmonellosisusually lasts 4 to 7 days, and most people recover without treatment. Insome cases Salmonella infection can enter the bloodstream leading tosepsis and can ultimately cause death if not treated. Children under theage of 5 years are most likely to get Salmonellosis. Children, theelderly, and immunocompromised are most likely to have severeinfections.

S. Hadar infections have been linked to catfish, sliced deli meats,turkey burgers, and handling of live poultry (e.g., chicks, ducklings,turkeys) (http://www.outbreakdatabase.com/).

S. Heidelberg infections have been linked to eggs, chicken, pork,salmon, and cheddar cheese. Recently, S. Heidelberg has been linked tooutbreaks in ground turkey, and Kosher broiled chicken livers(http://www.outbreakdatabase.com/). A routine inspection by the FDArecently (May, 2012) detected S. Heidelberg at a large Iowa poultryhouse used for egg production. S. Heidelberg in egg layers are a concernsince S. Heidelberg can infect eggs via the transovarian route in amanner similar to Salmonella Enteritidis, and S. Heidelberg has causedseveral egg associated outbreaks resulting in human illness and death.Eating eggs outside the home was identified as a primary risk factor forillness due to S. Heidelberg infection.

S. Heidelberg is one of the five serotypes most frequently isolated inhuman cases of salmonellosis in the U.S. The rise in prevalence of thisserovar has been accompanied by increasing antimicrobial resistance. S.Heidelberg appears to be a highly clonal serovar, with 34 of 36 globalisolates in the Salmonella enterica MLST database(http://mlst.ucc.ie/mlst/dbs/Senterica) having an identical sequencetype (ST15), and the other two (one from the US, and one from Australia)differing from this canonical serotype at only a single locus. A S.Heidelberg organism, if consumed in contaminated food, causessalmonellosis which is often characterized by fever, vomiting, diarrhea,abdominal cramps, and severe dehydration.

A PCR and gel-based molecular serotyping method for the detection andidentification of S. Hadar, S. Heidelberg, S. Enteritidis, and S.Typhimurium was designed based on detecting the combination ofO-antigen, phase 1 flagellar antigen (H1) and phase 2 flagellar antigengenes (H2). The O:H1:H2 assignment for S. Hadar and S. Heidelberg isC2:z10:e,n,x and B:r:1,2, respectively. However, because otherSalmonella enterica serotypes also carry each of these genes, thismethod is not sufficient to differentially identify a single serotypedue to cross-reactivity. In some cases a single base pair difference inthe flagellin gene sequence results in an amino acid change thatdisplays an epitope with a different serotype. The developers of thistest report that the H2 allelotyping primers cannot distinguish serovarsHeidelberg (B:r:1,2) from Bradford (B:r:1,5), Winneba (B:r:1,6), or Remo(B:r:1,7), and cannot distinguish serovar Hadar (C2:z10:e,n,x) fromGlostrup (C2:z10:e,n,z15).

Some S. Heidelberg-specific assays described in the literature aremolecular serotyping assays based on a set of four multiplex PCRreactions targeting five O-antigen loci, the fliC gene, and the fljBgene. Although very specific, the complexity of this assay makes itunsuitable for specific detection of S. Heidelberg. Another multiplextest known is an assay that detects both S. Heidelberg and S.Typhimurium performed in combination with another assay that onlydetects S. Typhimurium. A positive signal from the first, but not thesecond assay indicates the presence of S. Heidelberg. Two step assaysare always time consuming and can lead to errors.

Assays for rapid, sensitive, and specific detection of Salmonellaenterica pathogens are extremely important from both a public health andeconomic perspective. There exists a need for novel assays and methodsfor detecting and differentiating various serovars of Salmonellaenterica subsp. enterica such as S. Hadar and S. Heidelberg from otherSalmonella enterica serovars to test food and other contaminatedsamples. Some potential uses would be identification of a pathogen in acontaminated food to identify a contaminant; and identification of apathogen in a clinical sample to make a differential diagnosis of whatmicrobe is causing a particular disease.

SUMMARY

The present disclosure, in some embodiments, describes compositions,kits and methods of use thereof for detection of one or moremicroorganisms and/or strains and/or serotypes of a Salmonella entericasubsp. enterica. These Salmonella enterica subsp. enterica microbes arepresent as contaminants in a sample. Samples that can be tested bymethods of the disclosure to detect a microbial contaminant thereininclude but are not limited to a food sample (processed food samples andraw food samples), a beverage sample, an agricultural sample, a producesample, an animal sample, a clinical sample, an environmental sample, abiological sample, a water sample and an air sample.

Some embodiments relate to compositions comprising isolated nucleic acidsequences that are operable or able to specifically hybridize to nucleicacid regions that are uniquely found in a Salmonella enterica subsp.enterica microbes under conditions of hybridization. Nucleic acidregions uniquely found in a Salmonella enterica subsp. enterica serovar(including complementary regions thereof, fragments thereof, variants,alleles and sequences having 90% identity thereto) are referred toherein as “serovar specific target nucleic acids” or as “Salmonellaenterica subsp. enterica serovar specific target nucleic acids”. In someembodiments a serovar specific target nucleic acid is a S. Hadarspecific target nucleic acid or a S. Heidelberg specific target nucleicacid sequence.

In some embodiments, a Salmonella enterica subsp. enterica serovarspecific target nucleic acid is a fljB gene encoding the phase twoflagellin, or an allele (e.g., fljB_(e,n,x)), variant and/or fragmentthereof; a fliC gene encoding the phase one flagellin, or an allele(e.g. fliC_(z10)), variant and/or fragment thereof; an arsR geneencoding a transcriptional repressor (SeHA_C3265); a phage integrasegene (SeHA_C3266); a helicase-encoding gene (SeHA_C4894, SeHA_C4896, andSeHA_C4897); a type II restriction methylase encoding gene (SeHA_C4895);or SeHA_C4893, which encodes a hypothetical protein.

Some embodiments of the present disclosure describe compositionscomprising isolated oligonucleotide sequences. In some embodimentsoligonucleotide compositions of the disclosure are primer and/or probenucleic acid sequences that are specific to hybridize to a Salmonellaenterica subsp. enterica serovar specific target nucleic acid.

One embodiment describes compositions comprising isolated nucleic acidsequences having the nucleotide sequence of SEQ ID NOS: 1-12, fragmentsthereof, complements thereof, sequences having about 90% identity to theforegoing sequences and labeled derivatives thereof.

Some embodiments describe compositions comprising a set ofoligonucleotide primers for simultaneous use in a multiplexamplification (e.g., PCR) process for the detection of a Salmonellaenterica subsp. enterica serovar and comprise at least two primer sets,each primer set having at least a forward primer and at least a reverseprimer, all primers operable to hybridize to a serovar specific targetnucleic acids.

In one embodiment, a set of oligonucleotide primers for simultaneous usein a multiplex PCR process comprise primers operable to hybridize to andamplify (under appropriate amplification conditions) a S. Heidelbergserovar specific target nucleic acid. Some exemplary non-limiting setsof S. Heidelberg specific primers comprise at least two primer setsselected from a first primer set having SEQ ID NO: 1 and SEQ ID NO: 2; asecond primer set having SEQ ID NO: 4 and SEQ ID NO: 5; or sequencescomprising at least 90% nucleic acid sequence identity thereof, or alabeled derivative thereof.

In one embodiment, a set of oligonucleotide primers for simultaneous usein a multiplex PCR process comprise primers operable to hybridize to andamplify (under appropriate amplification conditions) a S. Hadar specifictarget nucleic acid. Some exemplary non-limiting set of S. Hadarspecific primers comprise at least two primer sets selected from a firstprimer set having SEQ ID NO: 7 and SEQ ID NO: 8; a second primer sethaving SEQ ID NO: 10 and SEQ ID NO: 11; or sequences comprising at least90% nucleic acid sequence identity thereof, or a labeled derivativethereof.

Fragments of nucleic acid sequences described herein include withoutlimitation nucleic acids having at least 10, at least 15, or at least 20contiguous nucleic acids of a nucleic acid sequence as described herein.Nucleic acid sequences of the disclosure, in some embodiments, areprimers and/or probes. In some embodiments, primers of the disclosuremay be degenerate primers. Primers and probes may be labeled. In someembodiments, isolated nucleic acid sequence compositions of thedisclosure may comprise one or more label, such as, but not limited to,a dye, a radioactive isotope, a chemiluminescent label, a fluorescentmoiety, a bioluminescent label, an enzyme, and combinations thereof. Insome embodiments primers and probes can comprise chemical and/orbiological derivatives of the sequences described here.

Some embodiments of the present disclosure describe methods fordetection of Salmonella enterica subsp. enterica serovar microorganismsin a sample and comprise detection of the presence of one or moreserovar specific target nucleic acid sequences. Some methods disclosedhere are singleplex methods and can detect the presence of one serovarspecific target region from nucleic acids present in a sample. Somemethods disclosed herein are multiplex methods which can simultaneouslydetect the presence of one or more targets of a serovar; and/orsimultaneously detect one or more targets of one or more serovars;and/or simultaneously detect the presence of one or more internalpositive controls (IPC) along with one or more serovar specific targetnucleic acid sequences, from nucleic acids present in a sample.

Some embodiments describe methods for detecting a Salmonella entericasubsp. enterica serovar microorganism in a sample comprising:hybridizing at least a first pair of nucleic acid amplification primersspecific to hybridize to a first serovar specific target nucleic acid, afragment thereof, a complements thereof, an allele thereof, and/or avariant thereof, wherein the first serovar specific target nucleic acidis present in a polynucleotide sequence present in the sample;amplifying at least the first serovar specific target nucleic acid or afragment, a complement, an allele and/or a variant thereof to obtain atleast a first amplified serovar specific product; and detecting thefirst amplified serovar specific product; wherein detection of the firstamplified serovar specific product is indicative of the presence of oneSalmonella enterica subsp. enterica serovar microorganism in the sample.Absence of an amplified product is indicative of the absence of thatSalmonella enterica subsp. enterica serovar microorganism in the sample.In some embodiments, at least two pairs of nucleic acid amplificationprimers can be used, wherein the second pair of nucleic acidamplification primers are specific to hybridize to a second serovarspecific target nucleic acid sequence and produce a second amplifiedserovar specific products, wherein detection of the first and/or thesecond amplified products is indicative of the presence of a Salmonellaenterica subsp. enterica in the sample.

Exemplary serovars detected are S. Heidelberg and S. Hadar, wherein thedetection of one or more S. Heidelberg specific target nucleic acids isindicative of the presence of a S. Heidelberg microorganism and whereinthe detection of one or more S. Hadar specific target nucleic acids isindicative of the presence of a S. Hadar microorganism in a sample.

One example embodiment method for detection of an S. Heidelberg in asample comprises: hybridizing at least a first pair of nucleic acidamplification primers comprising nucleic acids of SEQ ID NO: 1 and SEQID NO: 2 and/or primers having SEQ ID NO: 4 and SEQ ID NO: 5, and/orcomplements thereof, and/or sequences having at least 90% homologythereto, to at least a first target polynucleotide sequence present inthe sample; amplifying at least the first target polynucleotide sequenceor a fragment or a complement thereof to obtain at least one amplifiedtarget polynucleotide sequence; and detecting the at least one amplifiedtarget polynucleotide sequence; wherein detection of the at least oneamplified target polynucleotide sequence is indicative of the presenceof a S. Heidelberg organism in the sample. In some embodiments, at leasttwo primer sets selected from a primer set having SEQ ID NO: 1 and SEQID NO: 2 and/or a primer set having SEQ ID NO: 4 and SEQ ID NO: 5,and/or a primer set having complements of the foregoing sequences,and/or a primer set having sequences having at least 90% homology to theforegoing primer sets can be hybridized to sample nucleic acids andsubject to multiplex amplification conditions to obtain one or moreamplification products. Detection of one or both amplification productsis indicative of the presence of a S. Heidelberg serovar organism in thesample. In some embodiments, detection of both the first and the secondamplified products confirms the presence of S. Heidelberg.

A method to detect a S. Heidelberg can further comprise using a probe todetect the amplified target polynucleotide sequence wherein a probe cancomprises a sequence of SEQ ID NO: 3, SEQ ID NO: 6, fragments having atleast 10 contiguous nucleotides thereof, complements thereof, andsequences having at least 90% homology thereto. Hybridization of a probecan be used to identify a serovar.

One embodiments method for detection of an S. Hadar in a samplecomprises: hybridizing at least a first pair of nucleic acidamplification primers comprising nucleic acids of SEQ ID NO: 7 and SEQID NO: 8 and/or primers having SEQ ID NO: 10 and SEQ ID NO: 11, and/orcomplements thereof, and/or sequences having at least 90% homologythereto, to at least a first target polynucleotide sequence present inthe sample; amplifying at least the first target polynucleotide sequenceor a fragment or a complement thereof to obtain at least one amplifiedtarget polynucleotide sequence; and detecting the at least one amplifiedtarget polynucleotide sequence; wherein detection of the at least oneamplified target polynucleotide sequence is indicative of the presenceof a S. Hadar organism in the sample. In some embodiments, at least twoprimer sets selected from a primer set having SEQ ID NO: 7 and SEQ IDNO: 8 and/or a primer set having SEQ ID NO: 10 and SEQ ID NO: 11, and/ora primer set having complements of the foregoing sequences, and/or aprimer set having sequences having at least 90% homology to theforegoing primer sets can be hybridized to sample nucleic acids andsubject to multiplex amplification conditions to obtain one or moreamplification products. Detection of one or both amplification productsis indicative of the presence of a S. Hadar serovar organism in thesample. In some embodiments, detection of both the first and the secondamplified products confirms the presence of S. Hadar.

In some embodiments, an amplification can be preceded or simultaneouslycoupled with hybridization of a labeled probe, such as a TaqMan® probe,to a target nucleic acid prior to the commencement of the polymerasereaction.

A method to detect a S. Hadar can further comprise using a probe todetect the amplified target polynucleotide sequence. In someembodiments, a probe can comprises a sequence of SEQ ID NO: 9, SEQ IDNO: 12, fragments having at least 10 contiguous nucleotides thereof,complements thereof, and sequences having at least 90% homology thereto.Probes can be used to in additional method steps comprisingidentification of a serovar.

In some embodiments, not detecting any amplified product using methodsdescribed above can be used to exclude the presence of a microorganismof a particular serovar in a sample. In some embodiments, detectingand/or identifying an amplified nucleic acid comprises one or moremethods such as but not limited to hybridization, mass spectrometry,nanostring, microfluidics, chemiluminescence, enzyme technologies andcombinations thereof. Some embodiments comprise identifying theparticular microbial serovar and can comprise methods such as DNAsequencing. In some embodiment methods described here, nucleic acids(RNA/DNA) can be extracted from a sample suspected to contain amicroorganism to be detected prior to amplification or detection. Amethod can further comprise one or more steps such as: enrichment ofmicroorganisms in a sample prior to nucleic acid extraction; and/ornucleic acid extraction from microorganisms in a sample; and/or nucleicacid isolation from a sample; and/or nucleic acid purification from asample; and/or lysing bacterial cells from a sample prior tohybridization/amplification with primers and/or probes.

Methods of the present disclosure can be used to detect the presence ofa Salmonella enterica subsp. enterica in a sample such as but notlimited to a food sample, a beverage sample, an agricultural sample, aproduce sample, an animal sample, a human sample, a clinical sample, anenvironmental sample, a biological sample, a water sample and/or an airsample.

In some embodiments, methods of the disclosure can be performed on anautomated system. Automation decreases the time as well as efficiencyand allows processing multiples samples. Automated systems may compriseplatforms to automate sample preparation such as but not limited toMagMAX™ Express-96 Magnetic Particle Processor by Life TechnologiesCorporation; Pathatrix system by Life Technologies(http://www.matrixmsci.com/pathatrix.htm); MagNA Pure System by Roche;the QIAsymphony system by Qiagen, among others.

Detection in the methods above may be performed by a variety of methods,such as but not limited to, by a nucleic acid amplification reaction,the amplification reaction is an end-point determination, theamplification reaction is quantitative, the quantification is areal-time PCR, the real-time PCR is a SYBR® Green Assay or the real-timePCR is a TaqMan® Assay. Detection may in some embodiments be performedby hybridization using probes specific to amplified nucleic acidsequences encoding a target sequence. Combinations of amplification andhybridization may be used for detection according to some embodiments.

In some embodiments, hybridization may comprise at least a first probeand a second probe, the first probe further comprising a first label andsaid second probe further comprising a second label, wherein both labelsare selected from a dye, a radioactive isotope, a chemiluminescentlabel, and an enzyme, the dye comprises a fluorescein dye, a rhodaminedye, or a cyanine dye, the dye is a fluorescein dye and first probe islabeled with FAM™ dye and said second probe is labeled with VIC® dye.

Some embodiments describe kits suitable for identifying the presence ofa Salmonella enterica subsp. enterica serovar organism. A kit of thedisclosure can comprise one or more sets of primers operable tohybridize to and amplify a serovar-specific target nucleic acid. Anexample kit may comprise at least one pair (or more than one) of forwardand reverse PCR primer sets selected from a first primer set having SEQID NO: 1 and SEQ ID NO 2; a second primer set having SEQ ID NO: 4 andSEQ ID NO 5; a third primer set having SEQ ID NO: 7 and SEQ ID NO: 8;and/or a fourth primer set having SEQ ID NO: 10 and SEQ ID NO 11, and/orprimer sets with sequences comprising at least 90% nucleic acid sequenceidentity to the primer sets described here and/or primer sets withcomplementary sequences to the primer sets described here and/or alabeled derivative of any of the foregoing primer sets; optionally atleast one probe (or more than one) selected from probes selected fromSEQ ID NO: 3; SEQ ID NO: 6; SEQ ID NO: 9; and/or SEQ ID NO:12; and/orsequences comprising at least 90% nucleic acid sequence identitythereto; and/or sequences having complementary sequences thereto; and/ora labeled derivative of any of the foregoing sequences; and one or morecomponents selected from a group consisting of: at least one enzyme,dNTPs, at least one buffer, at least one salt, at least one controlnucleic acid sample and an instruction protocol. Different primers andprobes in a kit can be labeled with different labels to allow fordetection of different amplified products and/or hybridized products.

In the following detailed description, certain aspects and embodimentswill become evident. It should be understood that a given embodimentneed not have all aspects and features described herein. It should beunderstood that these aspects and embodiments are merely exemplary andexplanatory and are not restrictive of the present disclosure. It is tobe understood that both the foregoing general description and thefollowing detailed description are exemplary and explanatory only andare not restrictive of the present disclosure, as claimed.

DETAILED DESCRIPTION

For the purposes of interpreting of this specification, the followingdefinitions may apply and whenever appropriate, terms used in thesingular will also include the plural and vice versa. In the event thatany definition set forth below conflicts with the usage of that word inany other document, including any document incorporated herein byreference, the definition set forth below shall always control forpurposes of interpreting this specification and its associated claimsunless a contrary meaning is clearly intended (for example in thedocument where the term is originally used). It is noted that, as usedin this specification and the appended claims, the singular forms “a,”“an,” and “the,” include plural referents unless expressly andunequivocally limited to one referent. The use of “or” means “and/or”unless stated otherwise. The use of “comprise,” “comprises,”“comprising,” “include,” “includes,” and “including” are interchangeableand not intended to be limiting. Furthermore, where the description ofone or more embodiments uses the term “comprising,” those skilled in theart would understand that, in some specific instances, the embodiment orembodiments can be alternatively described using the language“consisting essentially of” and/or “consisting of.”

As used herein, the phrase “nucleic acid,” “nucleic acid sequence,”“oligonucleotide”, and “polynucleotides” are interchangeable and notintended to be limiting.

As used herein, the phrase “hybridization conditions” or “stringenthybridization conditions” refers to hybridization conditions which cantake place under a number of pH, salt and temperature conditions. The pHcan vary from 6 to 9, preferably 6.8 to 8.5. The salt concentration canvary from 0.15 M sodium to 0.9 M sodium, and other cations can be usedas long as the ionic strength is equivalent to that specified forsodium. The temperature of the hybridization reaction can vary from 30°C. to 80° C., preferably from 45° C. to 70° C. Additionally, othercompounds can be added to a hybridization reaction to promote specifichybridization at lower temperatures, such as at or approaching roomtemperature. Among the compounds contemplated for lowering thetemperature requirements is formamide. Thus, a polynucleotide istypically “substantially complementary” to a second polynucleotide ifhybridization occurs between the polynucleotide and the secondpolynucleotide. As used herein, “hybridization” or “specifichybridization” refers to hybridization between two polynucleotides understringent hybridization conditions.

As used herein, the term “polynucleotide” refers to a polymeric form ofnucleotides of any length, either ribonucleotides, deoxynucleotides, orpeptide nucleic acids (PNA), and includes both double- andsingle-stranded RNA, DNA, and PNA. A polynucleotide may includenucleotide sequences having different functions, including, forinstance, coding regions, and non-coding regions such as regulatoryregions. A polynucleotide can be obtained directly from a naturalsource, or can be prepared with the aid of recombinant, enzymatic, orchemical techniques. A polynucleotide can be linear or circular intopology. A polynucleotide can be, for example, a portion of a vector,such as an expression or cloning vector, or a fragment. An“oligonucleotide” refers to a polynucleotide of the present disclosure,typically a primer and/or a probe.

As used herein a “target-specific polynucleotide” refers to apolynucleotide having a target-binding segment that is perfectly orsubstantially complementary to a target sequence, such that thepolynucleotide binds specifically to an intended target withoutsignificant binding to non-target sequences under sufficiently stringenthybridization conditions. A target-specific polynucleotide can be e.g.,a primer or probe and the subject of hybridization with itscomplementary target sequence.

The term “target sequence”, “target specific nucleic acid” “targetsignature sequence” “target nucleic acid”, “target” or “targetpolynucleotide sequence” refers to a nucleic acid of interest. Exampletargets of interest in some embodiments of this application includeregions that are unique or specific to one or more Salmonella entericasubsp. enterica serovar encoding nucleic acids and fragments,complements and sequences with 90% homology thereto and include forexample nucleic acid sequences that are unique to serovars S. Heidelbergand S. Hadar. The target sequence can be a polynucleotide sequence thatis the subject of hybridization with a complementary polynucleotide,e.g. a primer or probe. The target sequence can be composed of DNA, RNA,an analog thereof, and including combinations thereof. The targetsequence may be known or not known, in terms of its actual sequence andits amplification can be desired. The target sequence may or may not beof biological significance. Typically, though not always, it is thesignificance of the target sequence which is being studied in aparticular experiment. As non-limiting examples, target sequences mayinclude regions of genomic DNA, regions of genomic DNA which arebelieved to contain one or more polymorphic sites, DNA encoding orbelieved to encode genes or portions of genes of known or unknownfunction, DNA encoding or believed to encode proteins or portions ofproteins of known or unknown function, DNA encoding or believed toencode regulatory regions such as promoter sequences, splicing signals,polyadenylation signals, etc.

As used herein an “amplified target polynucleotide sequence product” or“amplified product” refers to the resulting amplicon from anamplification reaction such as a polymerase chain reaction. Theresulting amplicon product arises from hybridization of complementaryprimers to a target polynucleotide sequence under suitable hybridizationconditions and the repeating in a cyclic manner the polymerase chainreaction as catalyzed by DNA polymerase for DNA amplification or RNApolymerase for RNA amplification.

As used herein, the “polymerase chain reaction” or PCR is a anamplification of nucleic acid consisting of an initial denaturation stepwhich separates the strands of a double stranded nucleic acid sample,followed by repetition of (i) an annealing step, which allowsamplification primers to anneal specifically to positions flanking atarget sequence; (ii) an extension step which extends the primers in a5′ to 3′ direction thereby forming an amplicon polynucleotidecomplementary to the target sequence, and (iii) a denaturation stepwhich causes the separation of the amplicon from the target sequence(Mullis et al., eds, The Polymerase Chain Reaction, BirkHauser, Boston,Mass. (1994). Each of the above steps may be conducted at a differenttemperature, preferably using an automated thermocycler (AppliedBiosystems LLC, a division of Life Technologies Corporation, FosterCity, Calif.). If desired, RNA samples can be converted to DNA/RNAheteroduplexes or to duplex cDNA by methods known to one of skill in theart.

As used herein, “amplifying” and “amplification” refers to a broad rangeof techniques for increasing polynucleotide sequences, either linearlyor exponentially. Exemplary amplification techniques include, but arenot limited to, PCR or any other method employing a primer extensionstep. Other nonlimiting examples of amplification include, but are notlimited to, ligase detection reaction (LDR) and ligase chain reaction(LCR). Amplification methods may comprise thermal-cycling or may beperformed isothermally. In various embodiments, the term “amplificationproduct” or “amplified product” includes products from any number ofcycles of amplification reactions.

In certain embodiments, amplification methods comprise at least onecycle of amplification, for example, but not limited to, the sequentialprocedures of: hybridizing primers to primer-specific portions of targetsequence or amplification products from any number of cycles of anamplification reaction; synthesizing a strand of nucleotides in atemplate-dependent manner using a polymerase; and denaturing thenewly-formed nucleic acid duplex to separate the strands. The cycle mayor may not be repeated.

Descriptions of certain amplification techniques can be found, amongother places, in H. Ehrlich et al., Science, 252:1643-50 (1991), M.Innis et al., PCR Protocols: A Guide to Methods and Applications,Academic Press, New York, N.Y. (1990), R. Favis et al., NatureBiotechnology 18:561-64 (2000), and H. F. Rabenau et al., Infection28:97-102 (2000); Sambrook and Russell, Molecular Cloning, ThirdEdition, Cold Spring Harbor Press (2000) (hereinafter “Sambrook andRussell”), Ausubel et al., Current Protocols in Molecular Biology (1993)including supplements through September 2005, John Wiley & Sons(hereinafter “Ausubel et al.”).

The term “label” refers to any moiety which can be attached to amolecule and: (i) provides a detectable signal; (ii) interacts with asecond label to modify the detectable signal provided by the secondlabel, e.g. FRET; (iii) stabilizes hybridization, i.e. duplex formation;or (iv) provides a capture moiety, i.e. affinity, antibody/antigen,ionic complexation. Labeling can be accomplished using any one of alarge number of known techniques employing known labels, linkages,linking groups, reagents, reaction conditions, and analysis andpurification methods. Labels include light-emitting compounds whichgenerate a detectable signal by fluorescence, chemiluminescence, orbioluminescence (Kricka, L. in Nonisotopic DNA Probe Techniques (1992),Academic Press, San Diego, pp. 3-28). Another class of labels arehybridization-stabilizing moieties which serve to enhance, stabilize, orinfluence hybridization of duplexes, e.g. intercalators, minor-groovebinders, and cross-linking functional groups (Blackburn, G. and Gait, M.Eds. “DNA and RNA structure” in Nucleic Acids in Chemistry and Biology,2.sup.nd Edition, (1996) Oxford University Press, pp. 15-81). Yetanother class of labels effect the separation or immobilization of amolecule by specific or non-specific capture, for example biotin,digoxigenin, and other haptens (Andrus, A. “Chemical methods for 5′non-isotopic labeling of PCR probes and primers” (1995) in PCR 2: APractical Approach, Oxford University Press, Oxford, pp. 39-54).

The terms “annealing” and “hybridization” are used interchangeably andmean the base-pairing interaction of one nucleic acid with anothernucleic acid that results in formation of a duplex or otherhigher-ordered structure. The primary interaction is base specific, i.e.A/T and G/C, by Watson/Crick and Hoogsteen-type hydrogen bonding.

The term “end-point analysis” refers to a method where data collectionoccurs only when a reaction is substantially complete.

The term “real-time analysis” refers to periodic monitoring during PCR.Certain systems such as the Applied Biosystems 7500 Real-Time PCR System(Applied Biosystems, Foster City, Calif.) conduct monitoring during eachthermal cycle at a pre-determined or user-defined point. Real-timeanalysis of PCR with FRET probes measures fluorescent dye signal changesfrom cycle-to-cycle, preferably minus any internal control signals.

The term “quenching” refers to a decrease in fluorescence of a firstmoiety (reporter dye) caused by a second moiety (quencher) regardless ofthe mechanism.

A “primer,” as used herein, is an oligonucleotide that is complementaryto a portion of target polynucleotide and, after hybridization to thetarget polynucleotide, may serve as a starting-point for anamplification reaction and the synthesis of an amplification product.Primers include, but are not limited to, spanning primers. A “primerpair” refers to two primers that can be used together for anamplification reaction. A “PCR primer” refers to a primer in a set of atleast two primers that are capable of exponentially amplifying a targetnucleic acid sequence in the polymerase chain reaction.

The term “probe” comprises a polynucleotide that comprises a specificportion designed to hybridize in a sequence-specific manner with acomplementary region of a specific nucleic acid sequence, e.g., a targetnucleic acid sequence. In certain embodiments, the specific portion ofthe probe may be specific for a particular sequence, or alternatively,may be degenerate, e.g., specific for a set of sequences. In certainembodiments, the probe is labeled. The probe can be an oligonucleotidethat is complementary to at least a portion of an amplification productformed using two primers.

The terms “complement” and “complementary” as used herein, refer to theability of two single stranded polynucleotides (for instance, a primerand a target polynucleotide) to base pair with each other, where anadenine on one strand of a polynucleotide will base pair to a thymine oruracil on a strand of a second polynucleotide and a cytosine on onestrand of a polynucleotide will base pair to a guanine on a strand of asecond polynucleotide. Two polynucleotides are complementary to eachother when a nucleotide sequence in one polynucleotide can base pairwith a nucleotide sequence in a second polynucleotide. For instance,5′-ATGC and 5′-GCAT are complementary.

A “label” refers to a moiety attached (covalently or non-covalently), orcapable of being attached, to an oligonucleotide, which provides or iscapable of providing information about the oligonucleotide (e.g.,descriptive or identifying information about the oligonucleotide) oranother polynucleotide with which the labeled oligonucleotide interacts(e.g., hybridizes). Labels can be used to provide a detectable (andoptionally quantifiable) signal. Labels can also be used to attach anoligonucleotide to a surface.

A “fluorophore” is a moiety that can emit light of a particularwavelength following absorbance of light of shorter wavelength. Thewavelength of the light emitted by a particular fluorophore ischaracteristic of that fluorophore. Thus, a particular fluorophore canbe detected by detecting light of an appropriate wavelength followingexcitation of the fluorophore with light of shorter wavelength.

The term “quencher” as used herein refers to a moiety that absorbsenergy emitted from a fluorophore, or otherwise interferes with theability of the fluorescent dye to emit light. A quencher can re-emit theenergy absorbed from a fluorophore in a signal characteristic for thatquencher, and thus a quencher can also act as a fluorophore (afluorescent quencher). This phenomenon is generally known as fluorescentresonance energy transfer (FRET). Alternatively, a quencher candissipate the energy absorbed from a fluorophore as heat (anon-fluorescent quencher).

As used herein the term “sample” refers to a starting material suspectedof harboring a particular microorganism or group of microorganisms. A“contaminated sample” refers to a sample harboring a pathogenic microbethereby comprising nucleic acid material from the pathogenic microbe.Examples of samples include, but are not limited to, food samples(including but not limited to samples from food intended for human oranimal consumption such as processed foods, raw food material, produce(e.g., fruit and vegetables), legumes, meats (from livestock animalsand/or game animals), fish, sea food, nuts, beverages, drinks,fermentation broths, and/or a selectively enriched food matrixcomprising any of the above listed foods), water samples, environmentalsamples (e.g., soil samples, dirt samples, garbage samples, sewagesamples, industrial effluent samples, air samples, or water samples froma variety of water bodies such as lakes, rivers, ponds etc.,), airsamples (from the environment or from a room or a building), forensicsamples, agricultural samples, pharmaceutical samples, biopharmaceuticalsamples, samples from food processing and manufacturing surfaces, and/orbiological samples.

Disclosed are compositions, assays, methods and kits for the specificdetection of Salmonella enterica subsp. enterica serovar microorganismsfrom samples including clinical samples, food samples, complex foodmatrices, water, a beverage sample, a fermentation broth, a forensicsample, an environmental sample (e.g., soil, dirt, garbage, sewage, air,or water), including food processing and manufacturing surfaces, and/orbiological samples.

A sample may be tested directly, or may be prepared or processed in somemanner prior to testing. For example, a sample may be processed toenrich any contaminating microbe and may be further processed toseparate and/or lyse microbial cells contained therein. Lysed microbialcells from a sample may be additionally processed or prepares toseparate, isolate and/or extract genetic material from the microbe foranalysis to detect and/or identify the contaminating microbe. In someembodiments described here, as sample may be subject to separation toinitially separate microbes of interest from other microbes and othersample components. For example, for complex food samples with complexcomponents separation methods can be used to separate microorganismsfrom food. Separated microbes from samples can also be enriched prior toanalysis. Analysis of a sample may include one or more molecularmethods. For example, according to some exemplary embodiments of thepresent disclosure, a sample may be subject to nucleic acidamplification (for example by PCR) using appropriate oligonucleotideprimers that are specific to one or more microbe nucleic acid sequencesthat the sample is suspected of being contaminated with. Amplificationproducts may then be further subject to testing with specific probes (orreporter probes) to allow detection of microbial nucleic acid sequencesthat have been amplified from the sample. In some embodiments, if amicrobial nucleic acid sequence is amplified from a sample, furtheranalysis may be performed on the amplification product to furtheridentify, quantify and analyze the detected microbe (determineparameters such as but not limited to the microbial strain,pathogenecity, quantity etc.).

As used herein “preparing” or “preparing a sample” or “processing” orprocessing a sample” refers to one or more of the following steps toachieve separation of microbes from sample components and in someembodiments optionally extraction and/or separation of a nucleic acidfrom a sample: (1) optional separation of bacterial cells from samplecomponents (such as a food sample), (2) optional bacterial enrichment,(3) optional cell lysis, and/or (4) optionally nucleic acid extractionand/or purification (e.g., DNA extraction, total nucleic acid extraction(i.e., DNA and RNA), genomic DNA extraction, RNA extraction). Types ofnucleic acid extracted include, but are not limited to, DNA, RNA, mRNAand miRNA.

As used herein, “presence” refers to the existence (and therefore to thedetection) of a reaction, a product of a method or a process (includingbut not limited to, an amplification product resulting from anamplification reaction), or to the “presence” and “detection” of anorganism such as a pathogenic organism or a particular strain or speciesof an organism.

As used herein, “detecting” or “detection” refers to the disclosure orrevelation of the presence or absence in a sample of a targetpolynucleotide sequence or amplified target polynucleotide sequenceproduct. The detecting can be by end point, real-time, enzymatic, and byresolving the amplification product on a gel and determining whether theexpected amplification product is present, or other methods known to oneof skill in the art.

The presence or absence of an amplified product can be determined or itsamount measured. Detecting an amplified product can be conducted bystandard methods well known in the art and used routinely. The detectingmay occur, for instance, after multiple amplification cycles have beenrun (typically referred to an end-point analysis), or during eachamplification cycle (typically referred to as real-time). Detecting anamplification product after multiple amplification cycles have been runis easily accomplished by, for instance, resolving the amplificationproduct on a gel and determining whether the expected amplificationproduct is present. In order to facilitate real-time detection orquantification of the amplification products, one or more of the primersand/or probes used in the amplification reaction can be labeled, andvarious formats are available for generating a detectable signal thatindicates an amplification product is present. For example, a convenientlabel is typically a label that is fluorescent, which may be used invarious formats including, but are not limited to, the use of donorfluorophore labels, acceptor fluorophore labels, fluorophores,quenchers, and combinations thereof. Assays using these various formatsmay include the use of one or more primers that are labeled (forinstance, scorpions primers, amplifluor primers), one or more probesthat are labeled (for instance, adjacent probes, TaqMan® probes,light-up probes, molecular beacons), or a combination thereof. Theskilled person in view of the present teachings will understand that inaddition to these known formats, new types of formats are routinelydisclosed. The present disclosure is not limited by the type of methodor the types of probes and/or primers used to detect an amplifiedproduct. Using appropriate labels (for example, different fluorophores)it is possible to combine (multiplex) the results of several differentprimer pairs (and, optionally, probes if they are present) in a singlereaction. As an alternative to detection using a labeled primer and/orprobe, an amplification product can be detected using a polynucleotidebinding dye such as a fluorescent DNA binding dye. Examples include, forinstance, SYBR® Green dye or SYBR® Gold dye (Molecular Probes). Uponinteraction with the double-stranded amplification product, suchpolynucleotide binding dyes emit a fluorescence signal after excitationwith light at a suitable wavelength. A polynucleotide binding dye suchas a polynucleotide intercalating dye also can be used.

A “target specific polynucleotide” of the present disclosure refers to anucleic acid sequence that is able to specifically hybridize to a geneand/or an allele and/or a portion thereof and/or a complement thereofthat encodes a unique target nucleic acid sequence specific to aSalmonella enterica subsp. enterica serovar under suitable hybridizationconditions and which does not hybridize with other nucleic acidsequences that do not encode for the unique target or portions thereofor complements thereof. In some embodiments, a “target-specificpolynucleotide” of the disclosure is a probe or primer sequencedescribed in SEQ ID NOS: 1-12. It is well within the ability of oneskilled in the art, using the present teachings, to determine suitablehybridization conditions based on probe length, G+C content, and thedegree of stringency required for a particular application.

It is expected that minor sequence variations in serovar specific targetnucleotide sequences associated with nucleotide additions, deletions andmutations, whether naturally occurring or introduced in vitro, would notinterfere with the usefulness of the various primer and probe nucleicacid sequences disclosed herein, as would be understood by one of skillin the art. Therefore, the scope of the present disclosure as claimed isintended to encompass minor variations in the sequences of describedhere and sequences having at least 90% homology to the primer and probesequences disclosed herein.

A probe may be RNA or DNA. Depending on the detection means employed,the probe may be unlabeled, radiolabeled, chemiluminescent labeled,enzyme labeled, or labeled with a dye. The probe may be hybridized witha sample in solution or immobilized on a solid support such asnitrocellulose, a microarray or a nylon membrane, or the probe may beimmobilized on a solid support, such as a silicon chip or a microarray.

Conditions that “allow” an event to occur or conditions that are“suitable” for an event to occur, such as hybridization, strandextension, and the like, or “suitable” conditions are conditions that donot prevent such events from occurring. Thus, these conditions permit,enhance, facilitate, and/or are conducive to the event. Such conditions,known in the art and described herein, may depend upon, for example, thenature of the nucleotide sequence, temperature, and buffer conditions.These conditions may also depend on what event is desired, such ashybridization, cleavage, or strand extension. An “extracted”polynucleotide refers to a polynucleotide that has been removed from acell. An “isolated” polynucleotide refers to a polynucleotide that hasbeen removed from its natural environment. A “purified” polynucleotideis one that is at least about 60% free, preferably at least about 75%free, and most preferably at least about 90% free from other componentswith which they are naturally associated.

The words “preferred” and “preferably” refer to embodiments of thepresent disclosure that may afford certain benefits, under certaincircumstances. However, other embodiments may also be preferred, underthe same or other circumstances. Furthermore, the recitation of one ormore preferred embodiments does not imply that other embodiments are notuseful, and is not intended to exclude other embodiments from the scopeof the present disclosure.

The terms “comprises” and variations thereof do not have a limitingmeaning where these terms appear in the description and claims. Unlessotherwise specified, “a,” “an,” “the,” and “at least one” are usedinterchangeably and mean one or more than one.

Also herein, the recitations of numerical ranges by endpoints includeall numbers subsumed within that range (e.g., 1 to 5 includes 1, 1.5, 2,2.75, 3, 3.80, 4, 5, etc.). The term “and/or” means one or all of thelisted elements or a combination of any two or more of the listedelements.

There are many known methods of amplifying nucleic acid sequencesincluding e.g., PCR. See, e.g., PCR Technology: Principles andApplications for DNA Amplification (ed. H. A. Erlich, Freeman Press, NY,N.Y., 1992); PCR Protocols: A Guide to Methods and Applications (eds.Innis, et al., Academic Press, San Diego, Calif., 1990); Mattila et al.,Nucleic Acids Res. 19, 4967 (1991); Eckert et al., PCR Methods andApplications 1, 17 (1991); PCR (eds. McPherson et al., IRL Press,Oxford); and U.S. Pat. Nos. 4,683,202, 4,683,195, 4,800,159 4,965,188and 5,333,675 each of which is incorporated herein by reference in theirentireties for all purposes.

Nucleic acid amplification techniques are traditionally classifiedaccording to the temperature requirements of the amplification process.Isothermal amplifications are conducted at a constant temperature, incontrast to amplifications that require cycling between high and lowtemperatures. Examples of isothermal amplification techniques are:Strand Displacement Amplification (SDA; Walker et al., 1992, Proc. Natl.Acad. Sci. USA 89:392 396; Walker et al., 1992, Nuc. Acids. Res. 20:16911696; and EP 0 497 272, all of which are incorporated herein byreference), self-sustained sequence replication (3SR; Guatelli et al.,1990, Proc. Natl. Acad. Sci. USA 87:1874 1878), the Qβ replicase system(Lizardi et al., 1988, BioTechnology 6:1197 1202), and the techniquesdisclosed in WO 90/10064 and WO 91/03573.

Examples of techniques that require temperature cycling are: polymerasechain reaction (PCR; Saiki et al., 1985, Science 230:1350 1354), ligasechain reaction (LCR; Wu et al., 1989, Genomics 4:560 569; Barringer etal., 1990, Gene 89:117 122; Barany, 1991, Proc. Natl. Acad. Sci. USA88:189 193), transcription-based amplification (Kwoh et al., 1989, Proc.Natl. Acad. Sci. USA 86:1173 1177) and restriction amplification (U.S.Pat. No. 5,102,784).

Other exemplary techniques include Nucleic Acid Sequence-BasedAmplification (“NASBA”; see U.S. Pat. No. 5,130,238), Qβ replicasesystem (see Lizardi et al., BioTechnology 6:1197 (1988)), and RollingCircle Amplification (see Lizardi et al., Nat Genet 19:225 232 (1998)).The amplification primers of the present disclosure may be used to carryout, for example, but not limited to, PCR, SDA or tSDA. Any of theamplification techniques and methods disclosed herein can be used topractice the claimed present disclosure as would be understood by one ofordinary skill in the art.

PCR is an extremely powerful technique for amplifying specificpolynucleotide sequences, including genomic DNA, single-stranded cDNA,and mRNA among others. Various methods of conducting PCR amplificationand primer design and construction for PCR amplification will be knownto those of skill in the art. Generally, in PCR a double-stranded DNA tobe amplified is denatured by heating the sample. New DNA synthesis isthen primed by hybridizing primers to the target sequence in thepresence of DNA polymerase and excess dNTPs. In subsequent cycles, theprimers hybridize to the newly synthesized DNA to produce discreetproducts with the primer sequences at either end. The productsaccumulate exponentially with each successive round of amplification.

The DNA polymerase used in PCR is often a thermostable polymerase. Thisallows the enzyme to continue functioning after repeated cycles ofheating necessary to denature the double-stranded DNA. Polymerases thatare useful for PCR include, for example, Taq DNA polymerase, Tth DNApolymerase, Tfl DNA polymerase, Tma DNA polymerase, Tli DNA polymerase,and Pfu DNA polymerase. There are many commercially available modifiedforms of these enzymes including: AmpliTaq® and AmpliTaq Gold® bothavailable from Applied Biosystems. Many are available with or without a3- to 5′ proofreading exonuclease activity. See, for example, Vent® andVent® (exo-) available from New England Biolabs.

Other suitable amplification methods include the ligase chain reaction(LCR) (e.g., Wu and Wallace, Genomics 4, 560 (1989) and Landegren etal., Science 241, 1077 (1988)), transcription amplification (Kwoh etal., Proc. Natl. Acad. Sci. USA 86, 1173 (1989)), and self-sustainedsequence replication (Guatelli et al., Proc. Nat. Acad. Sci. USA, 87,1874 (1990)) and nucleic acid based sequence amplification (NABSA).(See, U.S. Pat. Nos. 5,409,818, 5,554,517, and 6,063,603). The lattertwo amplification methods include isothermal reactions based onisothermal transcription, which produce both single-stranded RNA (ssRNA)and double-stranded DNA (dsDNA) as the amplification products in a ratioof about 30 or 100 to 1, respectively.

Several Salmonella enterica subsp. enterica serovars are known to causesalmonellosis in humans. Serotype definitions for Salmonella entericasubsp. enterica are known to the skilled artisan and are described forexample by Grimont et al. (Grimont P.A.D., Weill F: “Antigenic formulaeof Salmonella serovars.” In., 9th edn: WHO; 2007.). Some species ofSalmonella have the potential to be pathogenic to humans. Among theseare the serovars S. Heidelberg and S. Hadar which are commoncontaminants of turkey meats as well as catfish, sliced deli meats,turkey burgers, eggs, and other poultry (e.g., chicks, ducklings,turkeys) and cause salmonellosis which can be marked by gastroenteritis,fever, vomiting, diarrhea, abdominal cramps, and severe dehydration andin some instances the infection can advance to sepsis and othercomplications including death.

Currently known methods to detect microbes of serovar S. Hadar involveusing PCR and gel-based molecular serotyping techniques to detect acombination of O-antigen, phase 1 flagellar antigen and phase 2flagellar antigen genes (Hong Y, Liu T, Lee M D, Hofacre C L, Maier M,White D G, Ayers S, Wang L, Berghaus R, Maurer J J: “Rapid screening ofSalmonella enterica serovars Enteritidis, Hadar, Heidelberg andTyphimurium using a serologically-correlative allelotyping PCR targetingthe 0 and H antigen alleles,” BMC Microbiol 2008, 8:178). Antigen genesdescribed by Hong are shown in Table 1.

TABLE 1 Target Type Gene O-antigen C2 (6, 8) abe₂ H1 z10 fliC H2 e, n, xfljB

However, based on BLASTN searches performed herein, other Salmonellaenterica serotypes were also found to carry each of these genes (seeTable 2) and hence this method is not sufficient to differentiallyidentify a single serotype due to cross-reactivity.

TABLE 2 Other Salmonells enterica subsp. Target Type Gene entericamatching serotypes O-antigen C2 (6, 8) abe₂ Newport, Muenchen H1 z10fliC Haifa, Mbandaka, Lexington H2 e, n, x fljB Abortusequi, Chester,Mbandaka, Brandenburg, Mikawasima, Braenderup

One assay for detection of the serovar S. Heidelberg-specific describedin literature comprises molecular serotyping based on a set of fourmultiplex PCR reactions targeting five O-antigen loci, the fliC gene,and the fljB gene (Hong Y, Liu T, Lee M D, Hofacre C L, Maier M, White DG, Ayers S, Wang L, Berghaus R, Maurer JJ: “Rapid screening ofSalmonella enterica serovars Enteritidis, Hadar, Heidelberg andTyphimurium using a serologically-correlative allelotyping PCR targetingthe O and H antigen alleles,” BMC Microbiol 2008, 8:178). This PCR andgel-based molecular serotyping method for detection and identificationof S. Hadar, S. Heidelberg, S. Enteritidis, and S. Typhimurium is basedon detecting the combination of O-antigen, phase 1 flagellar antigen(H1) and phase 2 flagellar antigen genes (H2). The O:H1:H2 assignmentfor S. Hadar and S. Heidelberg is C2:z10:e,n,x and B:r:1,2,respectively. However, because other Salmonella enterica serotypes alsocarry each of these genes, this method is not sufficient todifferentially identify a single serotype due to cross-reactivity. Insome cases a single base pair difference in the flagellin gene sequenceresults in an amino acid change that displays an epitope with adifferent serotype. Hong Y. et al. report that the H2 allelotypingprimers cannot distinguish Heidelberg (B:r:1,2) from Bradford (B:r:1,5),Winneba (B:r:1,6), or Remo (B:r:1,7), or Hadar (C2:z10:e,n,x) fromGlostrup (C2:z10:e,n,z15). Hence, the complexity of this assay makes itunsuitable for specific detection of S. Heidelberg or S. Hadar.

Another multiplex assay described in literature is a combination of twoseparate assays: the first assay detects two serovars S. Heidelberg andS. Typhimurium followed by a second assay that only detects S.Typhimurium. A positive signal from the first assay combined with theabsence of a positive signal (i.e., a negative signal) from the secondassay indicates the presence of S. Heidelberg (see, McCarthy N, Reen FJ, Buckley J F, Frye J G, Boyd E F, Gilroy D: “Sensitive and rapidmolecular detection assays for Salmonella enterica serovars Typhimuriumand Heidelberg,” J Food Prot 2009, 72(11):2350-2357. However, this testbeing a two-step assay is time consuming and the potential for errors ineither step leads to unreliability.

The present disclosure describes novel compositions, kits and methodsfor detection and in some embodiments for differential detection, ofSalmonella enterica subsp. enterica serovars. Compositions, kits andmethods of the present disclosure provide the ability to detect and/ordistinguish between these microbial contaminants in samples includingcomplex food samples.

In one embodiment, bioinformatic and direct DNA sequencing comparisonsof several Salmonella enterica subsp. enterica serovar organisms wereconducted and unique loci specific to different serovars (unique locialso described herein as “serovar specific target nucleic acids”) wereidentified. Analysis to identify unique serovar specific target nucleicacids comprised testing an “Inclusion Panel” which comprised multiplegeographically and temporally diverse strains of a first serovar ofSalmonella enterica subsp. enterica and testing an “Exclusion Panel”comprising other Salmonella enterica subsp. enterica serotypes thatshare one or more alleles with the first serovar.

For example, for identification of unique S. Hadar serovar specifictarget nucleic acids, analysis comprised testing an “Inclusion Panel”which comprising multiple geographically and temporally diverse strainsof S. Hadar and testing an “Exclusion Panel” comprising other Salmonellaserotypes that share one or more alleles with S. Hadar, including theserovars Chester, Mbandaka, Brandenburg, Mikawasima, Braenderup,Newport, Haifa, Lexington, Muenchen, Istanbul, Chomedey, Abortusequi,and Glostrup.

Analysis of inclusion and exclusion panels and alignment of variousknown serovar sequences using custom algorithms identified several S.Hadar serovar specific target regions. Primer pairs of the disclosurewere then designed to each of the serovar specific target regions tospecifically amplify only the unique serovar specific target sequencesagainst both inclusion (organism to be detected, i.e., S. Hadar) andexclusion genomes (organisms not to be detected, non-S. Hadar serovarorganisms).

In another example, to identify sequences specific to S. Heidelberg, twogenomes were obtained from GenBank: the complete SL476 strain (CP001120,multidrug resistant), and the draft SL486 strain (ABEL00000000,antibiotic susceptible). These genomes were run through customalgorithms using a set of 50 non-Heidelberg S. enterica genomes(complete and draft public genomes, and draft internal assemblies) asthe exclusion set. This method identified 19 regions of the S.Heidelberg genome, comprising over 40 kb of sequence, that are conservedin both S. Heidelberg strains, but at least 20% divergent in all otheravailable Salmonella genomes. Some of these regions were located inclusters on the chromosome. To assess specificity of these sequencesbeyond S. enterica, these candidate nucleic acid signature regions werecompared by BLAST to the microbial subset of the GenBank nucleotidedatabase. Some of the identified 19 sequences had conservation withnumerous P22 phage sequences from other enteric bacteria, and were notconsidered any further. Regions with >80% identity to other sequences(mostly E. coli), were also removed from consideration and nucleic acidregions (target sequences) unique to S. Heidelberg serovar wereidentified. Primers and probes were then designed using the identifiedtarget sequences to achieve specific hybridization and amplification ofthese target sequences and/or portions thereof.

In one embodiment, unique serovar specific targets of Salmonellaenterica subsp. enterica comprise: a fljB gene encoding the phase twoflagellin, and/or an allele (e.g., fljB_(e, n, x)), a variant, acomplement and/or a fragment thereof; a fliC gene encoding the phase 1flagellin, and/or an allele (e.g., fliC_(z10)), a variant, a complementand/or a fragment thereof specific to S. Hadar; an arsR gene encoding atranscriptional repressor (SeHA_C3265); a phage integrase gene(SeHA_C3266); a helicase-encoding gene (SeHA_C4894, SeHA_C4896, andSeHA_C4897); a type II restriction methylase encoding gene (SeHA_C4895);or SeHA_C4893, which encodes a hypothetical protein, which are specificto S. Heidelberg. The S. Heidelberg identifiers (e.g., SeHA_CNNNN, whereN=a number) are unique identifiers in the NCBI “Gene” database athttp://www.ncbi.nlm.nih.gov/gene. These genes were identified on GenBankaccession NC_(—)011083.1 dated 27 Jan. 2012.

Several programs for designing primers such as Primer3 (Steve Rozen andHelen J. Skaletsky (2000) “Primer3” on the World Wide Web for generalusers and for biologist programmers as published in: Krawetz S, MisenerS (eds) Bioinformatics Methods and Protocols: Methods in MolecularBiology. Humana Press, Totowa, N.J., pp. 365-386), Primer Express®software (Applied Biosystems), and OLIGO 7 (Wojciech Rychlik (2007).“OLIGO 7 Primer Analysis Software” Methods Mol. Biol. 402: 35-60). Insome embodiments of the present disclosure, custom primer designingsoftware was used for primer designing and PCR primers and probes weredesigned for use in assays by real-time PCR to detect unambiguously,specifically and with great sensitivity Salmonella enterica subsp.enterica serovars.

In some embodiments, compositions comprising primer and/or probesequences comprise isolated nucleic acid sequences having the nucleotidesequence of SEQ ID NOS: 1-12, complements thereof and sequences havingabout 90% identity to the foregoing sequences. In some embodiments, thepresent disclosure describes designing degenerate primers. In someembodiments the present disclosure describes designing multiplex primersthat are suitable for multiplex amplification (PCR) type of assays. Insome embodiments, isolated nucleic acid sequence compositions of thedisclosure may further comprise one or more label, such as, but notlimited to, a dye, a radioactive isotope, a chemiluminescent label, afluorescent moiety, a bioluminescent label an enzyme, and combinationsthereof.

Some embodiments describe compositions comprising a set ofoligonucleotide primers for use in a multiplex amplification process(e.g. PCR) for detection of a Salmonella enterica subsp. entericaserovar, the set of oligonucleotide primers comprising: at least twoprimer sets, each primer set having at least a forward primer and atleast a reverse primer, that are operable to specifically hybridize to aserovar specific target nucleic acids. In some embodiments, primer setsdescribed herein are suitable for simultaneous multiplex amplificationreactions.

In some embodiments, a serovar specific target nucleic acid comprises aS. Heidelberg specific gene, an allele, a variant, and/or a fragment ora complement thereof. Exemplary primer sets for amplification and/ormultiplex amplification of a S. Heidelberg serovar target nucleic acidcomprise one or more primer sets selected from a first primer set havingSEQ ID NO: 1 and SEQ ID NO: 2; and/or a second primer set having SEQ IDNO: 4 and SEQ ID NO: 5; and/or primer sets with sequences comprising atleast 90% nucleic acid sequence identity to the foregoing primers,and/or primers comprising a labeled derivative of the foregoing primersets.

In some embodiments, a serovar specific target nucleic acid comprises aS. Hadar specific gene, an allele, a variant, and/or a fragment or acomplement thereof. Exemplary primer sets for multiplex amplification ofa S. Hadar serovar target nucleic acid comprise at least two primer setsselected from a first primer set having SEQ ID NO: 7 and SEQ ID NO: 8; asecond primer set having SEQ ID NO: 10 and SEQ ID NO: 11; and/or primersets with sequences comprising at least 90% nucleic acid sequenceidentity to any of the foregoing primer sets, and/or a primer set asdescribed additionally comprising a labeled derivative.

The specification describes methods for detection of Salmonella entericasubsp. enterica serovar organisms from a sample and also describesmethods to exclude the presence of a Salmonella enterica subsp. entericaserovar organism in a sample, wherein the detection of at least onenucleic acid sequence that is expressed in a particular serovar isindicative of the presence of a that serovar specific organism and theabsence of detection of any nucleic acid sequence unique to theparticular serovar is indicative of the absence of that serovar specificorganism in the sample.

In one embodiment, a method of detection of a Salmonella enterica subsp.enterica serovar microorganism comprises a) detecting the presence of aSalmonella enterica subsp. enterica serovar specific target nucleic acidsequence comprising: 1) contacting a sample with one or more probesspecific to hybridize to of a Salmonella enterica subsp. entericaserovar microorganism specific target nucleic acid and 2) detectinghybridization of the one or more probe. Example probes are described inSEQ ID NO: 3, SEQ ID NO: 6, SEQ ID NO: 9 and SEQ ID NO: 12. In someembodiments, detection of specific hybridization of probes having SEQ IDNO: 3 and/or SEQ ID NO: 6 and/or a probe having 90% homology theretoand/or having a labeled derivative is indicative of the presence of a S.Heidelberg microorganism. In some embodiments, detection of specifichybridization of probes having SEQ ID NO: 9 and/or SEQ ID NO: 12 and/ora probe having 90% homology thereto and/or having a labeled derivativeis indicative of the presence of a S. Hadar microorganism.

In one embodiment, a method for detection of a Salmonella entericasubsp. enterica serovar microorganism comprises: a) contacting a samplewith one or more sets of oligonucleotide primers specific to hybridizeto target nucleic acids specific to one or more Salmonella entericasubsp. enterica serovar specific target nucleic acid sequences; b)amplifying at least one Salmonella enterica subsp. enterica serovarspecific target nucleic acid sequence by a multiplex amplificationmethod to obtain one or more amplified Salmonella enterica subsp.enterica serovar specific nucleic acids; c) detecting the one or moreamplified Salmonella enterica subsp. enterica serovar specific nucleicacids or fragments or complements thereof; and d) optionally identifyingthe Salmonella enterica subsp. enterica serovar specific nucleic acid;wherein detecting the one or more amplified Salmonella enterica subsp.enterica serovar specific nucleic acids or fragments or complementsthereof is indicative of the presence of a Salmonella enterica subsp.enterica serovar microorganism in the sample.

In some embodiments of the present methods, one assay alone may not bedefinitive for detecting a Salmonella enterica subsp. enterica serovarorganism due to genomic similarity between the genomic regions of othernon-Salmonella or other Salmonella serovar organisms. Yet, when two (ormore) assays such as but not limited to the assays shown in Table 3 areused either in parallel or as a multiplex assay, e.g., in a real-timeTaqMan® assay, for example, where each probe in each of the two (ormore) assays has a different label for distinguishing results on areal-time PCR instrument, e.g., a 7500 Fast Real-Time PCR System(Applied Biosystems), a positive result from such an assay is indicativeof the presence of a particular Salmonella enterica subsp. entericaserovar organism.

In some embodiments, oligonucleotide primers that can be used in amultiplex method of the disclosure comprises two or more primer setsselected from a first primer set having SEQ ID NO: 1 and SEQ ID NO: 2; asecond primer set having SEQ ID NO: 4 and SEQ ID NO: 5; a third primerset having SEQ ID NO: 7 and SEQ ID NO: 8; or a fourth primer set havingSEQ ID NO: 10 and SEQ ID NO: 11 or sequences comprising at least 90%nucleic acid sequence identity thereof, or a labeled derivative thereof.In some embodiments, primers to amplify an internal positive control canalso be used simultaneously in the multiplex assay. Singleplex assayscomprise selecting one primer set from the primer sets described above.

In some embodiments, dual or multiplex (more than 2 assay sets) assayapproach can be used to detect and distinguish between two serovars. Forexample, multiplexing with primers specific to both serovars followed bydetection and/or identification of amplified nucleic acids indicates thepresence of one or both serovars in a sample. In some embodiments, amethod can comprise labeling a first primer set for detecting a firstserovar specific target nucleic acid with a first label and subsequentprimer sets for detecting additional serovar specific target nucleicacids with a second, a third, a fourth, etc. subsequent labels anddetecting the presence of amplified fragments wherein presence of one ormore serovars is identified by detecting a label of one or moreamplified products. In specific embodiments, one or more S. Heidelbergand S. Hadar specific amplification products can be detected, whereineach amplification product is labeled with a different label.

Methods, in some embodiments, can include multiplex assays such aspolymerase chain reactions, wherein hybridizing and amplifying of saidfirst pair of polynucleotide primers occurs in a first vessel and saidhybridizing and amplifying of said second pair of polynucleotide primersoccurs in a second vessel (and hybridizing and amplifying of subsequentpairs of primers in subsequent vessels) or can comprise hybridizing andamplifying of said first pair of polynucleotide primers and saidhybridizing and amplifying of said second pair of polynucleotide primers(and hybridizing and amplifying of subsequent pairs of primers) alloccurs in a single vessel, the detection is a real-time assay, thereal-time assay is a SYBR® Green dye assay or a TaqMan® assay.

A method of the disclosure can further comprise providing a first probeand a second probe (and additional probes such as a third probe and afourth probe and so on), wherein the first and second probes aredifferent from each other, the first probe operable to identify thefirst amplified target polynucleotide sequence and the second probeoperable to identify the second amplified target nucleotide sequence,the first probe further comprises a first label and said second probefurther comprises a second label, wherein both labels are selected froma dye, a radioactive isotope, a chemiluminescent label, and an enzyme,the dye comprises a fluorescein dye, a rhodamine dye, or a cyanine dye,the dye is a fluorescein dye and first probe is labeled with FAM™ dyeand said second probe is labeled with VIC® dye; and hybridizing thefirst and second probes to the PCR amplified fragments to detect thepresence of the first amplified target polynucleotide sequence and thesecond amplified target polynucleotide sequence from the sample.

In some embodiments of a method as described above, step d) foridentifying a Salmonella enterica subsp. enterica serovar specificnucleic acid comprises contacting the one or more amplified Salmonellaenterica subsp. enterica serovar specific nucleic acids, fragments orcomplements thereof with a probe specific to hybridize to at least oneof the amplified Salmonella enterica subsp. enterica serovar specificnucleic acids, fragments or complements thereof under conditions ofhybridization and wherein detection of hybridization is indicative ofthe identity of a Salmonella enterica subsp. enterica serovarmicroorganism in the sample. For example, detection of hybridizationwith a S. Heidelberg specific probe indicates the identity of theserovar as a S. Heidelberg and detection of hybridization with a S.Hadar specific probe indicates the identity of the serovar as a S.Hadar. Exemplary probes specific to hybridize to at least one of theamplified Salmonella enterica subsp. enterica serovar specific nucleicacids, fragments or complements thereof are SEQ ID NO:3, SEQ ID NO: 6,SEQ ID NO:9 or SEQ ID NO: 12 or sequences comprising at least 90%nucleic acid sequence identity thereof, or a labeled derivative thereof.

Identification can also be done by analyzing one or more amplificationproducts by methods such as but not limited to electrophoresis,hybridization, mass spectrometry, molecular barcoding, microfluidics,chemiluminescence, DNA sequencing and/or enzyme technologies

In one example embodiment, a method of detecting a S. Heidelbergmicroorganism in a sample comprises: a) contacting nucleic acids presentin a sample with at least one primer set, having one forward primer andone reverse primer, comprising primers selected from a first primer sethaving SEQ ID NO: 1 and SEQ ID NO 2 and/or a second primer set havingSEQ ID NO: 4 and SEQ ID NO: 5 and/or primer sets having sequences withat least 90% homology thereto, under conditions to amplify from thesample an S. Heidelberg specific target nucleic acid or a fragment or acomplement thereof and b) detecting at least one amplified nucleic acidamplified in steps a), wherein detection of at least one amplifiednucleic acid indicates the presence of a S. Heidelberg organism in thesample. In some embodiments, a multiplex amplification method using atleast two primer sets selected from the primers listed above is used anddetection of two amplified products is used for identification of S.Heidelberg. The multiplex method can further comprising additionallycontacting nucleic acids in the sample with a primer operable tohybridize to and amplify a positive control.

In one example embodiment, a method of detecting a S. Hadarmicroorganism in a sample comprises: a) contacting nucleic acids presentin the sample with at least one primer set, having one forward primerand one reverse primer, comprising primers selected from a first primerset having SEQ ID NO: 7 and SEQ ID NO 8 and/or sequences having at least90% homology thereto and/or a second primer set having SEQ ID NO: 10 andSEQ ID NO: 11 and/or sequences having at least 90% homology thereto,under conditions to amplify from the sample an S. Hadar specific targetnucleic acid or a fragment or a complement thereof and b) detecting atleast one amplified nucleic acid amplified in steps a), whereindetection of at least one amplified nucleic acid indicates the presenceof a S. Hadar organism in the sample. In some embodiments, a multiplexamplification method using at least two primer sets selected from theprimers listed above is used and detection of two amplified products isused for identification of S. Hadar. The multiplex method can furthercomprising additionally contacting nucleic acids in the sample with aprimer operable to hybridize to and amplify a positive control.

A method of the disclosure can further comprise processing a sample. Insome embodiments this can comprise steps such as but not limited to:nucleic acid extraction; and/or nucleic acid purification frommicroorganisms in a sample; and/or optional enrichment of microorganismsin a sample prior to nucleic acid extraction and/or purification.

In some embodiment methods, a sample to be tested for potentialcontamination can be tested directly or can be “prepared” or “processed”in some manner prior to molecular testing and analysis (such as by PCR).For example, a sample can be processed to separate and/or to enrich acontaminating microbe. A sample can also be further processed toseparate microbial nucleic acids from the remainder of the sample bylysing microbial cells. Lysing can be accomplished using a variety ofbuffers that can comprise lysing agents such as but not limited tochaotropic agents, and/or enzymatic agents and/or proteases. Lysedmicrobial cells from a sample can be additionally processed to separate,isolate and/or extract genetic material from the microbe prior to theamplification analysis methods described herein by several methods knownto the skilled artisan. For example, nucleic acid extraction can beperformed by kits and reagents from Life Technologies Corporation suchas the PrepSEQ™ Rapid Spin Sample Preparation Kit can be used to prepareDNA from food and/or environmental samples for use in PCR amplificationreactions. Using a simple spin protocol, the PrepSEQ™ Rapid Spinefficiently prepares microbial DNA from food matrices, by forming alysate with the DNA (but not extracting DNA), that is compatible for PCRamplification. The kit provides a fast, cost-effective solution forpreparing DNA from a broad range of sample types. The PrepSEQ® NucleicAcid Extraction Kit from Life Technologies produces high-qualitybacterial DNA samples for PCR-based detection from a wide range of foodand environmental samples.

Some embodiments can comprise one or more of the following steps toachieve separation of microbes and/or their nucleic acids from samplecomponents prior to analysis of microbial nucleic acids as describedherein: (1) optional bacterial enrichment to enrich certain types ofbacteria (e.g., by providing conditions to selectively increase onebacterial type), (2) optional bacterial cell lysis, (3) optional nucleicacid extraction and/or purification (e.g., DNA extraction, total nucleicacid extraction (i.e., DNA and RNA), genomic DNA extraction, RNAextraction using spin columns and/or buffers and/or other known methodsin the art).

In some embodiments, the disclosure describes workflows of methods fordetecting and identifying one or more Salmonella enterica subsp.enterica serovar microbes: (1) prepare a PCR, or Real-time PCR reactionmix, (2) amplify the signal in a PCR instrument, (3) analyze the PCRresults by visual inspection or software designed to simplify dataoutput.

Compositions and methods of the present disclosure are ideally suitedfor the preparation of kits. A kit suitable for detecting the presenceof a Salmonella enterica subsp. enterica serovar microorganism cancomprise at least one set of oligonucleotide primers for use in annucleic acid amplification process for the detection of a Salmonellaenterica subsp. enterica serovar specific nucleic acid. Some embodimentsdescribe a kit comprising: at least one pair of forward and reverse PCRprimer sets selected from a first primer set having SEQ ID NO: 1 and SEQID NO 2; a second primer set having SEQ ID NO: 4 and SEQ ID NO 5; athird primer set having SEQ ID NO: 7 and SEQ ID NO: 8; and/or a fourthprimer set having SEQ ID NO: 10 and SEQ ID NO 11, and/or sequencescomprising at least 90% nucleic acid sequence identity thereof, or alabeled derivative thereof; and optionally at least one probe selectedfrom probes selected from SEQ ID NO: 3, SEQ ID NO: 6, SEQ ID NO: 9 andSEQ ID NO:12 or sequences comprising at least 90% nucleic acid sequenceidentity thereof, or a labeled derivative thereof; and one or morecomponents selected from a group consisting of: at least one enzyme,dNTPs, at least one buffer, at least one salt, at least one controlnucleic acid sample and an instruction protocol. Some kits comprise atleast two primer sets described above. Some kits comprise all the primersets described above.

In some embodiments, kit primers can be labeled. A kit comprisingmultiple pairs of primers can have primer pairs each labeled withdifferent labels that can be detected separately. Probes comprised inkits of the disclosure can be labeled. If a kit comprises multipleprobes each probe can be labeled with a different label to allowdetection of different amplification products that are specificallyhybridized to by each different probe.

Kit components may be provided as solutions or as lyophilized powderswhich may be later reconstituted if needed in solutions and/or bufferswhich may also be provided. Components of kits may be individually andin various combinations comprised in one or a plurality of suitablecontainer means. It is within the scope of these teachings to providetest kits for use in manual applications or test kits for use withautomated sample preparation, reaction set-up, detectors or analyzers.In some embodiments, a kit amplification product may be further analyzedby methods such as but not limited to electrophoresis, hybridization,mass spectrometry, molecular barcoding, microfluidics, chemiluminescenceand/or enzyme technologies.

Those having ordinary skill in the art, in light of this specification,will understand that many modifications, alternatives, and equivalentsof the embodiments described above are possible. All such modifications,alternatives, and equivalents are intended to be encompassed herein.

EXAMPLES

The following procedures are representative examples of embodimentsaccording to the disclosure that may be employed for the detection of aSalmonella enterica subsp. enterica serovar. These examples are notintended to be limiting to the scope of the claims and/or the disclosurein any way.

Example 1 Compositions & Methods to Detect Salmonella enterica Subsp.enterica Serovar Organisms

The present example describes exemplary assays designed to detectSalmonella enterica subsp. enterica serovar organisms using probe andprimer sequences designed by the present inventors. Primer sequencescomprising pairs of forward and reverse primers and corresponding probesequences are shown in Table 3 below.

As shown in Table 3, an Assay ID number (such as 61163, 61172 etc.) isassigned to describe an associated primer pair (or primer pairs formultiplex assays) and associated probes that may be used for detectionof a Salmonella enterica subsp. enterica serovar specific targetsequence. These specific combinations of primer pairs and probesequences have designed to selectively amplify Salmonella entericasubsp. enterica serovar specific target nucleic acid sequence regionsfrom nucleic acids that are present in a sample suspected of beingcontaminated. In some embodiments these primer pairs are degenerate.

As shown in Table 3, a forward and reverse primer pair is shown in acolumn, which if used in an amplification reaction, will amplify thecorresponding target serovar specific nucleic acid. For example, AssayID number 61163 can be used to detect the presence of a S. Heidelbergserovar by: contacting a sample suspected of being contaminated with aforward primer, 61163F, having the nucleic acid sequenceCGGTCCCTGACTAAATTCAATACCA (SEQ ID NO: 1) and a reverse primer, 61163R,having the nucleic acid sequence TCAACTGACGACATTACCTGTTCTG (SEQ ID NO:2) under conditions to amplify a target nucleic acid sequence of anSeHA_C3265-3266 locus (or fragment or complement thereof). Meltingtemperatures (Tm) for forward and reverse primers are also shown inTable 3. In some embodiments, an amplified product amplified using theprimers of a column can be detected using a probe described in the samecolumn, for example in Assay ID 61163 a probe, 61163VIC, having thenucleic acid sequence ATGTGGTTCAGCTTTCTG (SEQ ID NO: 3) can be used.

Assay ID's of Table 2 can be combined to form multiplex assays. Forexample, one multiplex assay combines assays with Assay ID's 61163 withAssay ID 61172 and in some embodiments further with an assay to detectan internal positive control (assay not shown). Multiplex assays may beperformed by simultaneously contacting a sample with the one or moreprimer pairs. In some embodiments, multiplex assays can be performed inparallel or can be performed sequentially.

TABLE 3 Bac Primer  Multi- 1X Assay Track  or Probe Primer and Probe probe plex amp conc Target Thermal Name ID Names sequences 5′>3′Sequence label target  (bp) (nM) region Profile Salmonella 61163 61163FCGGTCCCTGACTAAATTCAATACCA VIC/ Salmonella 450 SeHA_ FAST enterica (SEQ ID NO: 1) MGB Heidelberg C326 svr. 61163VIC (VIC)ATGTGGTTCAGCTTTCTG200 5-3266 95 dC, Heidelberg (MGB) 2 min  multiplex (SEQ ID NO: 3)(1rep) 61163R TCAACTGACGACATTACCTGTTCTG 450 95 dC, (SEQ ID NO: 2) 30 sec61172 61172F TTGAGGCTGCATATTTGCTTTGAC FAM/ 450 SeHA_ 60 dC, (SEQ ID NO: 4) MGB C489 30 sec 3-4897 (40 reps) 61172FAM(6-FAM)TCGTTATTCCCAGGATAATG 200 (MGB) (SEQ ID NO: 5) 61172RCCGTTAAATCCGGCTTCATAGC 450 (SEQ ID NO: 6) Salmonella 61468 61468FTGCATTAGGCAACCCGACA FAM/ Salmonella 102 450 fljB e,  FAST enterica (SEQ ID NO: 7) MGB Hader n, x svr. 61468FAM (6-FAM))TACGGCGGCAGTCAAT 20095 dC, Hadar (SEQ ID NO: 9) 2 min  multiplex (1rep) 61468RCCCGCATCGGTATAACCACTTACA 450 95 dC, (SEQ ID NO: 8) 30 sec 61476 61476fGGATGCCTTAAAAGCGAGTGGTAT VIC/  61 450 fliC  60 dC,  (SEQ ID NO: 10) MGBz10 30 sec (40 reps)

Internal Positive Control (IPC) Assays can be used with the assaysdescribed in Table 3, in parallel or in multiplex. IPC primers andprobes are not described expressly herein.

Detecting can also comprise methods such as amplification,hybridization, mass spectrometry, nanostring, microfluidics,chemiluminescence, enzyme technologies and combinations thereof.Detecting steps using probes may comprise providing at least a firstprobe (and in some embodiments such as multiplex assays additionalprobes—such as a second probe, a third probe, a fourth probe etc.),wherein the first and second probes are different from each other, thefirst probe operable to identify the first amplified targetpolynucleotide sequence and the second probe operable to identify thesecond amplified target nucleotide sequence, the first probe furthercomprises a first label and said second probe further comprises a secondlabel, wherein both labels are selected from a dye, a radioactiveisotope, a chemiluminescent label, and an enzyme, the dye comprises afluorescein dye, a rhodamine dye, or a cyanine dye, the dye is afluorescein dye and first probe is labeled with FAM™ dye and said secondprobe is labeled with VIC® dye; and hybridizing the first and secondprobes to the PCR amplified fragments to detect the presence of thefirst amplified target polynucleotide sequence and the second amplifiedtarget polynucleotide sequence from the sample.

Example 2 Salmonella Detection in Turkey Meat Samples

The present example describes a sample preparation protocol incombination to prepare samples of turkey meat for detection of possibleSalmonella contamination.

In some embodiment methods prior to performing a PCR assay describedabove in Table 3 samples can be prepared. In one example, samplepreparation is by using a PrepSEQ™ Nucleic Acids Extraction Kit (LifeTechnologies Corporation) and a MagMAX™ Express-96 Deep Well MagneticParticle Processor (also of Life Technology Corporation) and comprises:

Enrichment Protocol for 375 g ground Turkey meat Sample: 1. For eachtest portion, add 1.2 L pre-warmed (37° C.) Buffered Peptone Water (BPW)enrichment broth to 375 g of sample. 2. Mix the solution by squeezingthe bag 10-15 times. Incubate at 37° C.±2° C. for 16-20 hours. 3. Afterincubation is complete, briefly shake the sample bags to ensure thebacteria are in solution. 4. Allow the bags to sit for 5 minutes so thatthe meat debris settles before removing aliquots.

Using the PrepSEQ® Nucleic Acid Extraction Kit for Food Testing (PN4428176) and the MagMAX™ Express-96 magnetic particle processor forpreparing samples.

Preparation of MagMAX™ Processor comprises: 1) Incubate a MagneticParticles tube at 37° C. for 10 minutes, vortex 5 to 10 seconds, andthen keep at room temperature until ready for use. White precipitateoccasionally forms in the Magnetic Particles tube. Extractionexperiments show that formation of precipitate does not affectperformance as long as the precipitate is redissolved and the MagneticParticles resuspended. Before using, always incubate the MagneticParticles tube at 37° C. for 10 minutes, then vortex to completelyresuspend. If after ten minutes the white precipitate is not completelydissolved, then longer incubation and higher temperatures (up to 50° C.)can be applied. 2) Prepare a Lysis Plate by carefully transferring 300ul of pre-enriched sample to the wells. 3) Prepare the following plates:a) Elution Plate: Add 120 μl of Elution Buffer to those wells of themicrotiter 96-well plate that correspond to the microtiter 96-well DWplate containing sample, as well as Lysis Buffer control. B) WashPlates: Prepare 2 Wash Plates by aliquoting 300 μl of Wash Buffer tothose wells of the microtiter 96-well plate that correspond to themicrotiter 96-well DW plate containing sample, as well as Lysis Buffercontrol. 4) To include Elution Buffer Control, aliquot 120 μl of ElutionBuffer to an extra empty well in the Elution Plate. 5) Prepare and Addthe binding Premix: a) Combine 2504, of PK Buffer with 325 μl of BindingBuffer and 254, of Magnetic Particles per sample; b) Vortex mixture for5 seconds, c) Add 600 μl of binding Premix to each well d) Load theplate into the instrument when instructed by MagMax-96 on-screen menu.In some embodiments, a program such as 4428176DWPrepSEQFA program(available with the magnetic processor) is then selected on the MagMAX™Express-96 magnetic particle processor. Press Start. Load the platesaccording to the readout. Verify orientation {A1 to A1}. A. Tip combs—inmicrotiter 96-well plate; press Start. B. Elution plate (120 uL ofElution Buffer)—In microtiter 96 well DW plate; press Start. C. Washplate 2 (300 μL of Wash Buffer)—In microtiter 96-well DW plate; pressStart. D. Wash plate 1 (300 μL of Wash Buffer—In microtiter 96-well DWplate; press Start. E. Lysis plate (sample in PK Buffer and bindingPreMix)—In microtiter 96-well DW plate; press Start. When samplepreparation is complete, the message “Enjoy your DNA” is displayed onthe screen. Remove Elution Plate. Proceed for PCR.

PCR Procedure can be performed using a Custom TaqMan® SalmonellaHeidelberg Assay Kit. Kit contents are set forth in Table 4 below:

TABLE 4 Kit Component Description Custom TaqMan ® Assay 1 rack of 96lyophilized assays (12 Salmonella beads 8-tube strips) containingSalmonella Heidelberg Heidelberg specific probes and Assay Beadsprimers, internal positive control and complete reagents for Real-TimePCR

PCR Procedure: a. Create a plate document (select AbsoluteQuantification (Standard Curve) from Assay drop-down list. Refer toAppendix 1 below and the appropriate instrument user guide for details.b. Create or select the following dye detectors with the Quencher Dyeset to (none) or Non-Fluorescent: FAM—Salmonella Heidelberg target #1;VIC—Salmonella Heidelberg target #2; NED—Internal Positive Control. c.Associate Dyes with each reaction. d. Set thermal cycling conditionsaccording to the following conditions: Stage 1: 95.0° C., 2:00 minutes;Stage 2: 40 repeats of [95.0° C. for 3 sec; 60.0° C. for 3 sec] e. SetSample Volume to 30 μl. f. Select the “Fast” Run Mode for your 7500Fastinstrument.

Prepare Real-Time PCR reactions as follows: a. Prepare assay beads.Remove and label an appropriate number of 8-strip tubes from the ziplock storage pouch. If needed, gently tap the tubes to move all of theassay beads to the bottom of all tubes. b. Prepare samples and controls.Thaw all reagents and place on ice. Determine the total volume of sampleand controls that you need for the target assay. Each reaction requires30 μL of sample. c. Carefully remove the caps from the 8-tube strips anddiscard the caps. Pipette samples or controls (30 μl) into tubescontaining assay beads. Use a new pipette tip for each different sample.d. Seal each tube completely with the transparent optical strip capsprovided in the kit. Strips are compatible with 7500 Fast Instrument. e.Mix by vortexing for 5 seconds at high speed. f. Spin down at 200×g for20 seconds to collect tube contents at bottom of the tubes.

Run the reactions by: a. Open the instrument loading block and place theprepared tubes or plate in the Real-Time PCR instrument. b. Open theplate document that corresponds to the reaction plate (created in Step 1above). c. Close the instrument loading block and start the run. Analyzethe results.

Example 3 Detection of S. Hadar

Methods of the present disclosure were used to screen for S. Hadar. Thepresent example describes an embodiment for detection from anenvironmental sample and comprises: 1. An environmental sample (e.g.,boot swab) is placed in a stomacher bag. 2. 225 mL of modifiedtetrathionate media (TT) with iodine-potassium iodide (IKI) andbrilliant green (BG) supplements are added to sample. 3. Sample is mixedthoroughly for a minimum of 15 seconds. 4. Sample is incubated at 35-37°C. for at least 15 h. 5. At the end of the incubation period samples areremoved from the incubator. The bags are squeeze a few times to ensuresample is mixed and to let any debris settle. 6. Proceed with samplepreparation as described for example in Example 1 using the PrepSEQ®Nucleic Acid Extraction Kit for Food Testing (PN 4428176) and theMagMAX™ Express-96 magnetic particle processor for preparing samplesfollowing instructions as outlined in the PrepSEQ® Nucleic AcidExtraction Kit Protocol, using the 4428176DWPrepSEQFA script. Exactenrichment time and the appropriateness of the media should be validatedfor each sample matrix to be tested.

PCR Procedure comprises using a Custom TaqMan® Salmonella Hadar AssayKit Contents. Kit Components include: Custom TaqMan® Salmonella HadarAssay, Beads, Assaybeads, 1 rack of 96 lyophilized assays (12 8-tubestrips) containing Salmonella Hadar specific probes and primers,internal positive control and complete reagents for Real-Time PCR.

PCR Protocol: Prepare Plate document (AB instruments) a. Create a platedocument (select Absolute Quantification (Standard Curve) from Assaydrop-down list. Refer to Appendix 1 below and the appropriate instrumentuser guide for details. b. Create or select the following dye detectorswith the Quencher Dye set to (none) or Non-Fluorescent: FAM—SalmonellaHadar target #1, VIC—Salmonella Hadar target #2, NED—Internal PositiveControl c. Associate Dyes with each reaction. d. Set thermal cyclingconditions according to the following conditions: Stage 1: 95.0° C.,2:00 minutes Stage 2: 40 repeats of [95.0° C. for 3 sec; 60.0° C. for 3sec]. e. Set Sample Volume to 30 μl. f. Select the “Fast” Run Mode foryour 7500Fast instrument. 2. Prepare Real-Time PCR reactions: a. Prepareassay beads. Remove and label an appropriate number of 8-strip tubesfrom the zip lock storage pouch. If needed, gently tap the tubes to moveall of the assay beads to the bottom of all tubes. b. Prepare samplesand controls. Thaw all reagents and place on ice. Determine the totalvolume of sample and controls that you need for the target assay. Eachreaction requires 30 μL of sample. c. Carefully remove the caps from the8-tube strips and discard the caps. Pipette samples or controls (300into tubes containing assay beads. Use a new pipette tip for eachdifferent sample. d. Seal each tube completely with the transparentoptical strip caps provided in the kit.

Run the reactions as follows: a. Open the instrument loading block andplace the prepared tubes or plate in the Real-Time PCR instrument. b.Open the plate document that corresponds to the reaction plate (createdin Step 1 above). c. Close the instrument loading block and start therun.

Analyze results: a. View the amplification plots for all reactions tomake sure they appear normal. b. Under Analysis Settings, for “Alldetectors” (FAM, VIC, and NED) select Autobaseline. c. Under AnalysisSettings, for FAM and VIC detectors, select Manual Ct. For FAM and VICdetectors, Set Threshold value to 0.50. For the NED detector, setthreshold value to 0.3. d. Click Analyze.

Ct cutoffs: 1. For the FAM and VIC detectors, appropriate Ct cutoffvalues at dRn=0.5 are applied. For initial testing, a Ct cutoff value of35.69 for both detectors is used. 2. For the NED detector, any Ct<40 atdRn=0.3 is considered positive (+). The expected Ct range for the IPC is30-35.

All publications and patent applications cited above are incorporated byreference in their entirety for all purposes to the same extent as ifeach individual publication or patent application were specifically andindividually indicated to be so incorporated by reference. Although thepresent disclosure has been described in some detail by way ofillustration and example for purposes of clarity and understanding, itwill be apparent that certain changes and modifications may be practicedwithin the scope of the appended claims.

1-20. (canceled)
 21. A composition comprising: at least one pair ofsynthetic forward and reverse PCR primer sets selected from a firstprimer set having SEQ ID NO: 1 and SEQ ID NO 2, and a second primer sethaving SEQ ID NO: 4 and SEQ ID NO:
 5. 22. The composition of claim 21,comprising both the first and second set of primers.
 23. The compositionof claim 21, further comprising at least one labeled probe selected fromSEQ ID NO: 3 and SEQ ID NO: 6, or full complements thereof.
 24. Thecomposition of claim 21 further comprising at least one pair ofsynthetic forward and reverse PCR primer sets selected from a thirdprimer set having SEQ ID NO: 7 and SEQ ID NO: 8; and a fourth primer sethaving SEQ ID NO: 10 and SEQ ID NO 11, full complements thereof or alabeled derivative thereof.
 25. The composition of claim 24 furthercomprising at least one labeled probe selected from SEQ ID NO: 9 and SEQID NO:12, or full complements thereof.
 26. A kit for the detection of aSalmonella enterica subsp. enterica serovar microorganism comprising: atleast one pair of synthetic forward and reverse PCR primer sets selectedfrom a first primer set having SEQ ID NO: 1 and SEQ ID NO 2, and asecond primer set having SEQ ID NO: 4 and SEQ ID NO: 5, at least onepair of synthetic forward and reverse PCR primer sets selected from athird primer set having SEQ ID NO: 7 and SEQ ID NO: 8; and a fourthprimer set having SEQ ID NO: 10 and SEQ ID NO 11, full complementsthereof or a labeled derivative thereof; at least one labeled probeselected from SEQ ID NO: 9 and SEQ ID NO:12, or full complementsthereof; at least one labeled probe selected from SEQ ID NO: 3 and SEQID NO: 6, or full complements thereof; and one or more componentsselected from a group consisting of: at least one enzyme, dNTPs, atleast one buffer, at least one salt, at least one pair of syntheticprimers specific to hybridize to and amplify an internal positivecontrol, at least one control nucleic acid sample and an instructionprotocol.
 27. A method for detection of a Salmonella enterica subsp.enterica serovar S. Hadar microorganism comprising: a) contacting asample with one or more sets of synthetic oligonucleotide primersspecific to hybridize to target nucleic acids specific to S. Hadarserovar specific target nucleic acid sequences selected from a firstprimer set having SEQ ID NO: 7 and SEQ ID NO: 8; and a second primer sethaving SEQ ID NO: 10 and SEQ ID NO: 11, full complements thereof, or alabeled derivative thereof; b) contacting the sample with at least oneset of oligonucleotide primers specific to hybridize to an internalpositive control specific nucleic acid sequence; c) optionallycontacting the sample with one or more labeled probes specific tohybridize to at least one of the S. Hadar specific nucleic acids,fragments or complements thereof, the probe selected from SEQ ID NO:9 orSEQ ID NO: 12, full complements thereof, or sequences comprising atleast 90% nucleic acid sequence identity thereto; d) amplifying at leastone S. Hadar specific target nucleic acid sequence and the internalpositive control specific sequence by a multiplex amplification method;e) detecting the one or more amplified S. Hadar specific nucleic acidsor fragments or complements thereof; and f) optionally identifying theS. Hadar specific nucleic acid; wherein detecting the one or moreamplified S. Hadar specific nucleic acids, fragments or complementsthereof is indicative of the presence of a Salmonella enterica subsp.enterica serovar S. Hadar microorganism in the sample.
 28. The method ofclaim 27, wherein the oligonucleotide primers have at least 90% nucleicacid sequence identity to the sequences of primer set one or primer settwo and the probes have a 100% nucleic acid identity to the probesequences of claim
 27. 29. The method of claim 27, wherein the labeledprobes have at least a 90% nucleic acid identity to the probe sequencesof claim 27, and the oligonucleotide primers have a 100% nucleic acidsequence identity to the sequences of primer set one or primer set two.30. The method of claim 27, wherein the sample is a food sample, abeverage sample, an agricultural sample, a produce sample, an animalsample, a clinical sample, an environmental sample, a biological sample,a water sample and an air sample.
 31. The method of claim 27 furthercomprising steps of: nucleic acid extraction from the microorganism inthe sample; and optional enrichment of the microorganisms in the sampleprior to nucleic acid extraction.
 32. The method of claim 27, whereinidentifying the S. Hadar specific nucleic acid comprises contacting theone or more amplified S. Hadar specific nucleic acids, fragments orcomplements thereof with a probe specific to hybridize to at least oneof the amplified S. Hadar specific nucleic acids, fragments orcomplements thereof under conditions of hybridization and whereindetection of hybridization with the probe is indicative of the presenceof a S. Hadar microorganism in the sample.
 33. The method of claim 32,wherein the probe specific to hybridize to at least one of the amplifiedS. Hadar specific nucleic acids, comprises SEQ ID NO:9 or SEQ ID NO: 12or a labeled derivative thereof.
 34. The method of claim 27, furthercomprising contacting the sample with at least one primer set specificto hybridize to a least one S. Heidelberg specific target nucleic acidsequence, selected from a third primer set having SEQ ID NO: 1 and SEQID NO 2, a fourth primer set having SEQ ID NO: 4 and SEQ ID NO: 5, underconditions to amplify an S. Heidelberg specific sample target nucleicacid or a fragment or a complement thereof; and detecting at least oneamplified S. Heidelberg specific nucleic acid sequence, whereindetection of the at least one amplified S. Heidelberg specific nucleicacid sequence indicates the presence of a S. Heidelberg organism in thesample.
 35. The method of claim 27, wherein the amplifying isquantitative.
 36. The method of claim 35, wherein the quantification isby a real-time polymerase chain reaction (PCR) assay.
 37. The method ofclaim 27, performed using a kit, the kit comprising: at least one pairof synthetic forward and reverse PCR primer sets selected from a firstprimer set having SEQ ID NO: 7 and SEQ ID NO: 8; and/or a second primerset having SEQ ID NO: 10 and SEQ ID NO 11, full complements thereof or alabeled derivative thereof; at least one pair of primers specific tohybridize to and amplify the internal positive control; at least oneprobe selected from probes selected from SEQ ID NO: 9 and SEQ ID NO:12,full complements thereof, or a labeled derivative thereof; and one ormore components selected from a group consisting of: at least oneenzyme, dNTPs, at least one buffer, at least one salt, at least onecontrol nucleic acid sample and an instruction protocol.
 38. The methodof claim 37, the kit further comprising: at least one pair of forwardand reverse PCR primers selected from SEQ ID NO: 1 and SEQ ID NO 2; andSEQ ID NO: 4 and SEQ ID NO 5, full complements thereof, or a labeledderivative thereof; and optionally at least one labeled probe selectedfrom SEQ ID NO: 3 and SEQ ID NO: 6 full complements thereof, or alabeled derivative thereof.